TEQC (version 3.12.0)

coverage.correlation: Coverage correlation plot

Description

Visualization of target coverage correlations between pairs of samples.

Usage

coverage.correlation(coveragelist, normalized = TRUE, plotfrac = 0.001, seed = 123, labels, main, pch = ".", cex.labels, cex.pch = 2, cex.main = 1.2, cex.corr, font.labels = 1, font.main = 2, ...)

Arguments

coveragelist

List where each element is the output of function coverage.target, where option perBase had to be set to TRUE.

normalized

if TRUE, correlation of normalized target coverages will be shown; original coverages otherwise

plotfrac

numeric value between 0 and 1. Coverages for a fraction of plotfrac of all target bases are shown.

seed

seed for random selection of plotfrac bases

labels

sample names that are written in the diagonal panels; if missing, names of coveragelist are taken; if those are NULL, "sample 'i'" is shown

main

main title

pch

plot symbol for the scatter plots

cex.labels, cex.pch, cex.main

sizes of sample labels, plot symbols, main title

cex.corr

size of the correlation values; if missing, sizes are made proportionally to the values of (positive) correlation.

font.labels, font.main

fonts for sample labels and main title

...

further graphical parameters, e.g. limits and symbol color for the scatter plots

Value

coverage values for pairs of samples. The lower panels show the respective Pearson correlation coefficients, calculated using all coverage values (even if not all of them are shown in the scatter plot).

Details

If normalized = TRUE, the function calculates normalized coverages: per-base coverages divided by average coverage over all targeted bases. Normalized coverages are not dependent on the absolute quantity of reads and are hence better comparable between different samples or even different experiments.

See Also

coverage.target, covered.k, coverage.hist, coverage.density, coverage.uniformity, coverage.plot

Examples

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## simulate another sample
r <- sample(nrow(reads), 0.1 * nrow(reads))
reads2 <- reads[-r,,drop=TRUE]
Coverage2 <- coverage.target(reads2, targets, perBase=TRUE)

## coverage uniformity plot
covlist <- list(Coverage, Coverage2)
coverage.correlation(covlist, plotfrac=0.1)